from what I know, if you put your own ~/.xinitrc file, it will skip executing files from /etc/X11/xinit/xinitrc.d/ directory. If it's true for FreeBSD, this might be not the best approach.
This is not accurate. There is a template in /usr/local/etc/X11/xinit called xinitrc that should be used to make your .xinitrc file because it reads files in xinitrc.d
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